Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks

Abstract

Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r 4 energy transfer distance (r) dependency versus the 1/r 6 dependency seen for a single donor–acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.

Synthesis of Substituted Cy5 Phosphoramidite Derivatives and Their Incorporation into Oligonucleotides Using Automated DNA Synthesis

“… 8 Within these structures, a variety of parameters can be iteratively modified and tested either jointly or independently including that of D/A ratios, D/A spacing, number of ET steps, relative dye orientation, interactions with other dyes, structural dimensionality (planar vs 3D), dye density, and so forth. 8 − 10 Cumulatively, this provides a powerful system to develop design strategies to optimally harvest light and then focus it on the nanoscale. To exploit exciton delocalization, DNA structures such as Holliday junctions allow the cyanine dyes to strongly interact and provide access to intriguing optical phenomena such as displaying J- and H-aggregate behavior along with large Davydov splitting.…”

Determining the Cytosolic Stability of Small DNA Nanostructures In Cellula

“…E ae accounts for the direct excitation of both the D and R dyes (see the Supporting Information). , The difference in initial D quench and E ae between structural classes arises since the crosshairs’ dyes can be placed linearly close to each other on the same arm, while the tetrahedron’s architecture dictates that the dyes be placed on different arms to correctly report structural degradation. The FRET efficiency, and therefore structural integrity, is subsequently reported as an A/D ratio.…”

Determination of association equilibrium constant from single molecule fluorescence localization microscopy

“…Besides this evidence, the capability of Cy3.5 (donor) and AlexaFluo647 (acceptor) to act as a FRET pair was also demonstrated in the literature by measurement of the fluorescence lifetime shortening of Cy3.5 from 1.6 ns when isolated, to ca. 0.6 ns in the presence of AlexaFluor647 [20].…”